Contacts of the helix formed by residues 364 - 376 (chain X) in PDB entry 1FM6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 364 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330X LEU* 4.4 1.8 - - + -
334X MET* 3.5 30.7 - - + -
339X VAL* 4.3 2.9 - - + -
353X LEU* 4.1 27.4 - - + -
362X ASP* 3.3 1.0 - - - +
363X PHE* 1.3 109.3 - - + +
365X GLU* 1.3 63.0 + - - +
366X PRO 3.5 0.4 - - - -
367X LYS* 3.0 13.4 + - - +
368X PHE* 3.0 40.2 + - + -
504X BRL 3.5 56.3 - - + +
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Residues in contact with GLU 365 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350X ARG* 2.6 48.0 + - - +
354X LYS* 2.9 46.2 + - + +
361X GLY 5.4 0.2 - - - +
362X ASP* 3.7 17.7 + - + +
364X MET* 1.3 77.6 - - - +
366X PRO* 1.3 65.4 - - + +
368X PHE* 3.0 6.6 + - - +
369X GLU* 2.9 45.5 + - - +
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Residues in contact with PRO 366 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362X ASP 3.2 18.6 - - - +
363X PHE* 3.8 7.0 - - - +
364X MET 3.6 2.7 - - - -
365X GLU* 1.3 91.6 - - + +
367X LYS* 1.3 66.5 + - + +
369X GLU* 3.3 16.8 - - - +
370X PHE* 3.0 29.1 + - - +
445X ILE* 3.8 15.8 - - + +
448X GLU* 3.9 24.5 - - + +
452X LEU* 6.2 1.1 - - + -
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Residues in contact with LYS 367 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327X TYR* 3.7 43.1 - - + -
330X LEU* 4.3 7.9 - - + -
334X MET* 3.9 18.6 - - + +
363X PHE* 2.6 33.7 + - - +
364X MET* 3.0 13.9 + - + +
366X PRO* 1.3 85.7 - - + +
368X PHE* 1.3 59.5 + - - +
370X PHE* 3.5 9.1 + - - +
371X ALA* 3.0 28.2 + - - +
445X ILE* 4.3 14.5 + - + +
449X HIS* 2.8 40.1 + - - +
452X LEU* 5.0 1.6 - - - +
504X BRL 5.3 1.6 - - - -
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Residues in contact with PHE 368 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334X MET* 3.6 28.5 - - + -
335X ASN 3.8 13.5 - - - -
336X LYS* 5.6 0.2 - - - -
338X GLY* 3.5 36.6 - - - -
339X VAL* 3.8 18.4 - - + -
350X ARG* 3.5 48.2 - - + +
353X LEU* 3.8 22.7 - - + -
364X MET* 3.0 33.1 + - + -
365X GLU* 3.0 6.5 + - - +
367X LYS* 1.3 74.5 - - - +
369X GLU* 1.3 64.8 + - - +
371X ALA* 3.3 4.5 + - + +
372X VAL* 3.2 28.7 + - - +
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Residues in contact with GLU 369 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350X ARG* 3.9 15.0 + - - +
365X GLU* 2.9 30.1 + - - +
366X PRO* 3.3 23.0 - - - +
368X PHE* 1.3 78.7 - - - +
370X PHE* 1.3 62.5 + - - +
372X VAL* 3.5 12.9 + - - +
373X LYS* 3.6 23.0 + - - +
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Residues in contact with PHE 370 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327X TYR* 3.8 28.3 - - + -
328X THR* 4.2 4.9 - - - -
331X ALA* 4.4 3.4 - - + -
366X PRO 3.0 17.7 + - - +
367X LYS* 3.7 7.6 - - - +
369X GLU* 1.3 75.4 - - - +
371X ALA* 1.3 69.9 + - + +
373X LYS* 3.3 13.2 + - - +
374X PHE* 2.9 62.6 + + + +
438X LYS* 4.2 14.1 - - + -
441X ASP* 4.2 21.1 - - + -
442X LEU* 3.5 35.2 - - + -
445X ILE* 4.0 20.9 - - + -
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Residues in contact with ALA 371 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331X ALA* 3.8 25.8 - - + -
334X MET* 3.7 24.9 - - + -
335X ASN* 6.0 1.8 - - - +
367X LYS 3.0 18.7 + - - +
368X PHE* 3.6 7.2 - - + +
369X GLU 3.3 0.4 - - - -
370X PHE* 1.3 78.6 - - + +
372X VAL* 1.3 54.3 + - + +
374X PHE* 4.4 0.2 - - - -
375X ASN* 2.7 47.1 + - - +
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Residues in contact with VAL 372 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335X ASN 5.4 1.3 - - - -
336X LYS* 3.7 44.4 - - + +
350X ARG* 4.5 14.4 - - - +
368X PHE* 3.2 17.4 + - + +
369X GLU* 3.7 8.7 - - - +
370X PHE 3.2 0.2 - - - -
371X ALA* 1.3 75.6 - - + +
373X LYS* 1.3 67.8 + - + +
375X ASN* 4.1 5.0 - - - +
376X ALA* 3.2 23.3 + - + +
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Residues in contact with LYS 373 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379U ASP* 2.9 46.2 + - + +
369X GLU* 3.6 21.6 + - - +
370X PHE* 3.3 14.5 + - - +
372X VAL* 1.3 79.4 - - + +
374X PHE* 1.3 63.1 + - - +
376X ALA* 3.4 18.0 - - - +
377X LEU* 4.0 5.7 + - - +
438X LYS* 3.8 22.1 + - - +
441X ASP* 3.5 15.2 + - - +
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Residues in contact with PHE 374 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X LYS* 6.2 2.7 - - - -
328X THR* 3.8 24.2 - - + -
331X ALA* 4.3 14.8 - - + -
370X PHE* 2.9 47.7 + + + +
371X ALA* 3.8 3.8 - - - +
373X LYS* 1.3 73.4 - - - +
375X ASN* 1.3 65.4 + - - +
376X ALA 3.0 1.8 - - - -
377X LEU* 2.8 31.9 + - + +
378X GLU 4.2 0.2 + - - -
379X LEU* 3.7 27.9 + - + +
384X LEU* 4.0 15.7 - - + -
387X PHE* 4.0 13.5 - + - -
435X LEU* 3.9 18.4 - - + -
438X LYS* 3.6 28.6 - - + +
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Residues in contact with ASN 375 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X LYS* 4.3 22.1 + - - +
331X ALA* 3.1 36.0 + - - +
332X SER* 4.3 0.5 + - - -
334X MET 3.4 16.2 + - - -
335X ASN* 4.7 4.4 - - - +
336X LYS* 6.4 0.2 - - - +
371X ALA* 2.7 32.0 + - - +
372X VAL* 4.1 4.4 - - - +
374X PHE* 1.3 76.7 - - - +
376X ALA* 1.3 54.2 + - - +
377X LEU 2.9 0.2 - - - -
378X GLU* 2.8 32.3 + - - +
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Residues in contact with ALA 376 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372X VAL* 3.2 13.8 + - + +
373X LYS* 3.4 17.0 - - - +
374X PHE 3.0 0.6 - - - -
375X ASN* 1.3 76.1 - - - +
377X LEU* 1.3 60.3 + - + +
378X GLU* 3.2 11.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il